P416: DNA METHYLATION-BASED CHARACTERIZATION OF ACUTE MYELOID LEUKEMIA POINTS TOWARDS KDM3B AS A 5Q HAPLOINSUFFICIENCY CANDIDATE
Authors: Katherine Kelly, Etienne Sollier, Anna Riedel, Linda Welte, Ekaterina Jahn, Hartmut Döhner, Konstanze Döhner, Pavlo Lutsik, Christoph Plass
Journal: HemaSphere (2023)

Background: Epigenetic enzymes, including histone modifiers and regulators of DNA methylation, are among the most frequent targets for mutations and structural variations in acute myeloid leukemia (AML). However, studies of complex karyotype AML, an aggressive subgroup defined by ≥3 unrelated chromosome abnormalities in the absence of other class-defining genetic abnormalities, have focused largely on its genetic rather than epigenetic characteristics. Within this subgroup, the most common abnormality is a deletion in the long arm of chromosome 5; an early event in leukemogenesis, which is invariably associated with poor clinical outcome and therapy resistance. While several candidate 5q tumor suppressors have been previously investigated, the pathogenic mechanisms underlying this deletion have not yet been elucidated. Aims: Here we aimed to assess the utility of DNA methylation profiles to improve the molecular classification of AML, with a focus on patients with complex karyotype. Methods: A reference-free methylome deconvolution method (MeDeCom) was applied to a cohort of 480 older AML patients which had been profiled by Infinium MethylationEPIC array. This approach allows decomposition of bulk methylomes to reveal a set of latent methylation components (LMCs) that might otherwise be obscured within epigenetically heterogeneous tumors. To decipher their likely origin, each methylation component was then interpreted by comparison to known cell-type-specific methylomes, and association with mutational and cytogenetic features. Results: Deconvolution of the AML methylome identified a distinct hypermethylation signature enriched in del5q AML. This encouraged us to further investigate candidate 5q tumor suppressor genes from an epigenetic perspective. Based on the overlap of deleted 5q segments in own and public datasets, we defined a minimally deleted region within 5q31.2, which peaks at a locus encoding the H3K9me1/2 demethylase, KDM3B. Differential gene expression analysis comparing del5q to 5q-retaining AML identified KDM3B as the most significantly downregulated of all genes within the minimally deleted interval. We thus hypothesized that KDM3B depletion could result in an increase in H3K9me1/2 and consequently trigger de novo DNA methylation at its targets, giving rise to the observed hypermethylation signature. Supporting this model, the del5q methylation signature correlated not only with reduced KDM3B gene expression but also with increased expression of its opposing H3K9me1/2 methyltransferases, EHMT2 (G9a) and PRDM16, and their downstream effector of de novo DNA methylation, DNMT3B. Furthermore, we could support our hypothesis by comparison to AML subgroups whose epigenetic alterations have already been described: Firstly, we note that the del5q methylome shows similarity to IDH mutant AML; a subgroup in which KDM3B activity is inhibited due to its metabolic dependency on alpha-ketoglutarate. Secondly, we found a similar methylation signature in patients overexpressing MECOM (EVI-1), an oncogene which is known to drive DNA hypermethylation through cooperation with DNMT3B. Summary/Conclusion: Our findings suggest that haploinsufficiency of KDM3B might represent an underlying epigenetic event in deletion 5q AML. We hypothesize that the resulting imbalance in H3K9me1/2 could confer epigenetic plasticity that might favor leukemic progression.Keywords: Complex aberrant karyotype, DNA methylation, AML